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From Computational Biophysics to Systems Biology

June 6 - 9 2006, Jülich, Germany



Over the last few decades the scope of biology has changed from categorizing experimental observations to understanding the underlying mechanisms. This is at least in part due to the increasing use of computers. Computers allow us to study single macromolecules, the interaction between various biomolecules, or their regulation in the cell. For many medical and pharmaceutical applications such as the understanding of desease pathways or the working of drugs at the level of an individual cell one would like an integration of these simulations - situated at a molecular level - into a functioning model of cells. This is one of the big challenges in computational biology requiring both new hardware and new techniques.

The many benefits of such an extension of computational biophysics into systems biology motivated the workshop that the research group "Computational Biology and Biophysics" held June 6-9, 2006 at the John von Neumann Institute for Computing in Jülich, Germany. Specifically, the workshop targeted the following general areas at the interface between (computational) biophysics and systems biology:

  • Protein folding (both structure prediction and mechanics)
  • Mis-folding and aggregation
  • Interaction between proteins and other molecules
  • Assembly of nano-structures, multi-protein, protein-DNA/RNA complexes
  • Cellular systems at the molecular level



Tuesday 06.06.2006

08:00Pick up in Aachen
10:00 - 10:15"Supercomputing at NIC", Thomas Lippert, Director NIC
10:15 - 10:30"From Computational Biophysics to Systems Biology", Ulrich Hansmann

Morning Session (Chair: U.H.E Hansmann)

10:30 - 11:30Harold Scheraga, The Two Aspects of the Protein Folding Problem
11:30 - 11:40Organizational remarks
11:40 - 12:00Coffee break
12:00 - 12:30Adam Liwo, Optimization of the united-residue UNRES force field for Langevin dynamics
12:30 - 14:00Lunch

Afternoon Session (Chair: J.H. Meinke)

14:00 - 14:45Tetsu Narumi, A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3
14:45 - 15:15 Cezary Czaplewski, Multiplexed-replica exchange molecular dynamics with UNRES force-field as an effective method for exploring the conformational energy landscape of proteins
15:15 - 15:45Coffee break
15:45 - 16:15Mariusz Makowski, Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. Tests with simple spherical systems
16:15 - 16:45Stanislaw Oldziej, Optimizing the UNRES force field for the prediction of proteins
16:45 - 17:15Michael Bachmann, Reduction to the simplest - The complexity of minimalistic heteropolymer models
17:15 - 17:45Dominik Gront, High accuracy method to protein backbone reconstruction
18:00 - 20:00Welcome Reception
20:00Bus to Aachen

Wednesday 07.06.2006

08:00Pick up in Aachen

Morning Session (Chair: T. Narumi)

09:00 - 9:45Wolfgang Wenzel, De novo protein structure prediction and folding
09:45 - 10:15Martin Mönnigmann, Protein Loop Structure Prediction With Flexible Stem Geometries
10:15 - 10:45Walter Nadler, Molecular Transport Through Channels and Pores: Effects of In-Channel Interactions and Blocking
10:45 - 11:15Coffee break
11:15 - 12:00Gordon Crippen, Cluster Distance Geometry and Protein Folding
12:00 - 12:30Giovanni La Penna, Modelling protein-DNA interactions in chromatin
12:30 - 14:00Lunch

Afternoon Session (Chair: Adam Liwo)

14:00 - 14:45Anders Irbäck, Protein folding and aggregation studied using an all-atom model with a simplified energy function
14:45 - 15:15Inta Liepina, Molecular dynamics study of two ABL-SH3 domain peptides amyloid formation
15:15 - 15:45Coffee break
15:45 - 16:15Siegfried Höfinger, A Very General Solvation Model for BioMolecular Simulation
16:15 - 16:45Magdalena Gruziel, From microscopic Monte-Carlo simulations to macroscopic solvation models
17:00 - 19:00Poster Session (beverages and snacks provided)
19:00Bus to Aachen

Thursday 08.06.2006

08:00Pick up in Aachen

Morning Session (Chair: A. Irbäck)

09:00 - 09:30Matthias Stein, Integrating Structural and Kinetic Enzymatic Information in Systems Biology
09:30 - 10:00Jesus Izaguirre, Inferring Protein-Protein Interactions from Data and Domain Docking
10:00 - 10:45Roland Eils, Computational Systems Biology
10:45 - 11:15Coffee break
11:15 - 11:45Anton Feenstra, Sub-type Specific Sites for SMAD Receptor Binding Identified by Sequence Comparison using "Sequence Harmony"
11:45 - 12:15Daniele Dell'Orco, In silico screening of mutational effects on Enzyme-Inhibitor affinity: a docking-based approach
12:15 - 12:45Francesco Guerrieri, Ab initio simulations of the Cu binding sites on the N-terminal
12:45 - 14:00Lunch

Afternoon Session (Chair: O. Zimmermann)

14:00 - 14:45Ruhong Zhou, Dewetting Transition and Hydrophobic Collapse in Protein Aggregates
15:00Leaving for Aachen
15:45Tour of the cathedral
17:30Tour of downtown Aachen
19:00Dinner in Aachen

Friday 09.06.2006

08:00Pick up in Aachen

Morning Session (Chair: G. Crippen)

09:00 -9:45Yuko Okamoto, Generalized-Ensemble Algorithms and Membrane Protein Structure Predictions
09:45 - 10:15Yuguang Mu, A new method of replica exchange method for protein folding in explicit water
10:15 - 10:45Caroline Taylor, Using simple fluid wetting as a model for cell spreading
10:45 - 11:15Coffee break
11:15 - 12:00A. Kolinski, Modeling protein structure, dynamics and thermodynamics with reduced representation of conformational space
12:00 - 12:30Wolfhard Janke, Adsorption phenomena at organic-inorganic interfaces
12:30 - 14:00Lunch

Afternoon Session (Chair: U.H.E. Hansmann)

14:00 - 14:30Phanourios Tamamis, Conformational analysis of compstatin with molecular dynamics simulations in explicit water
14:30 - 15:15Avijit Ghosh, From Simulation to Therapy: A Systems Biology Approach to Oncogene Detection and Drug Design
15:15 - 15:45Coffee break
15:45 - 16:30Social: Opening game of the World Cup 2006 Germany against Costa Rica (Begin 18:00 ZDF)
20:30Bus to Aachen leaves after the game (Return to Aachen in time to watch Poland vs. Ecuador)